Phage Genome Annotation Using the RAST Pipeline
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.
Key wordsPhage Genome annotation RAST Functional annotation Gene predictions
This work was supported by grants from the National Science Foundation MCB-1330800 and DUE-1323809 to RAE. BED was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004.
- 1.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75CrossRefPubMedPubMedCentralGoogle Scholar
- 2.Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason Iii JA, Stevens R, Vonstein V, Wattam AR, Xia F (2015) RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365CrossRefPubMedPubMedCentralGoogle Scholar
- 9.Noguchi H, Taniguchi T, Itoh T (2008) MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15:387–396Google Scholar
- 21.Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong EF, Dutilh BE, Rohwer F, Dinsdale EA (2012) Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol 14:3043–3065CrossRefPubMedGoogle Scholar